Input and runtime details for job 6527768 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
54	0.004897	0.3024	b1949	fliQ	-8.93	0.181731	208 -- 239	7 -- 38	flagellar biosynthesis protein		_____________207_______________________________240\n_____________\|_________________________________\|\n5'-UUC...GACAC__________UC__________G__C__AA___AUGAA...UUA-3'\n______________CUGAA_UCGG__AUGAUGAUGG_GA_UG__GCG\n______________\|\|\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|::_:\|_\|\|__\|\|\|\n______________GACUU_AGUC__UACUACUAUU_UU_AC__CGC\n3'-UUU...GUAGA_____A____CC__________G__U__G____AGAAAG-5'\n_____________\|_________________________________\|\n_____________39________________________________6\n	222 -- 228	17 -- 23	-27.1148 kcal/mol	8.82457 kcal/mol	9.35859 kcal/mol	207 240@LB@ \| \|@LB@5'-UUC...GACAC UC G C AA AUGAA...UUA-3'@LB@ CUGAA UCGG AUGAUGAUGG GA UG GCG@LB@ \|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|\|:: :\| \|\| \|\|\|@LB@ GACUU AGUC UACUACUAUU UU AC CGC@LB@3'-UUU...GUAGA A CC G U G AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -8.93 kcal/mol@LB@Hybridization Energy -27.1148 kcal/mol@LB@Unfolding Energy - mRNA 8.82457 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 208 -- 239@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 17 -- 23@LB@
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@LB@
71	0.006638	0.3087	b3857	mobA	-12.61	0.042607	253 -- 264	7 -- 18	molybdopterin-guanine dinucleotide synthase		_____________252__________265\n_____________\|____________\|\n5'-UCC...AGCCA________G___GCGUA...AAC-3'\n______________GACGAAUG_GCG\n______________:\|\|:\|\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	254 -- 260	11 -- 17	-15.9619 kcal/mol	2.14186 kcal/mol	1.20891 kcal/mol	252 265@LB@ \| \|@LB@5'-UCC...AGCCA G GCGUA...AAC-3'@LB@ GACGAAUG GCG@LB@ :\|\|:\|\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -15.9619 kcal/mol@LB@Unfolding Energy - mRNA 2.14186 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 253 -- 264@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
75	0.006972	0.3087	b4348	hsdS	-13.63	0.027959	190 -- 211	7 -- 29	specificity determinant for hsdM and hsdR		_____________189_____________________212\n_____________\|_______________________\|\n5'-CUG...UUGGU_______A_____________G_GAAAU...UAA-3'\n______________GGGGUGA_GG_AAUGAGUGCG_G\n______________\|\|\|:\|\|\|_\|:_\|\|::\|:\|\|\|\|_\|\n______________CCCUACU_CU_UUGUUUACGC_C\n3'-UUU...UAAGU_______A__A__________G_AGAAAG-5'\n_____________\|_______________________\|\n_____________30______________________6\n	203 -- 209	9 -- 15	-24.9713 kcal/mol	3.9222 kcal/mol	7.41901 kcal/mol	189 212@LB@ \| \|@LB@5'-CUG...UUGGU A G GAAAU...UAA-3'@LB@ GGGGUGA GG AAUGAGUGCG G@LB@ \|\|\|:\|\|\| \|: \|\|::\|:\|\|\|\| \|@LB@ CCCUACU CU UUGUUUACGC C@LB@3'-UUU...UAAGU A A G AGAAAG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -24.9713 kcal/mol@LB@Unfolding Energy - mRNA 3.9222 kcal/mol@LB@Unfolding Energy - sRNA 7.41901 kcal/mol@LB@@LB@Position - mRNA 190 -- 211@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
77	0.007102	0.3087	b0832	gsiD	-8.78	0.192254	77 -- 85	7 -- 15	glutathione ABC transporter permease		_____________76________86\n_____________\|_________\|\n5'-UUG...CGUAG_________AUUAC...GAU-3'\n______________AAAUGCGUG\n______________\|\|\|\|\|\|\|:\|\n______________UUUACGCGC\n3'-UUU...UAUUG_________AGAAAG-5'\n_____________\|_________\|\n_____________16________6\n	79 -- 85	7 -- 13	-12.0627 kcal/mol	2.10506 kcal/mol	1.17837 kcal/mol	76 86@LB@ \| \|@LB@5'-UUG...CGUAG AUUAC...GAU-3'@LB@ AAAUGCGUG@LB@ \|\|\|\|\|\|\|:\|@LB@ UUUACGCGC@LB@3'-UUU...UAUUG AGAAAG-5'@LB@ \| \|@LB@ 16 6@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -12.0627 kcal/mol@LB@Unfolding Energy - mRNA 2.10506 kcal/mol@LB@Unfolding Energy - sRNA 1.17837 kcal/mol@LB@@LB@Position - mRNA 77 -- 85@LB@Position - sRNA 7 -- 15@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 7 -- 13@LB@
92	0.009361	0.3104	b3652	recG	-7.88	0.265686	265 -- 278	7 -- 20	ATP-dependent DNA helicase		_____________264_____________279\n_____________\|_______________\|\n5'-CAA...ACUUA________C______AAAAU...UGC-3'\n______________GUAACAAA_UG_GCG\n______________:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UAUUGUUU_AC_CGC\n3'-UUU...ACUAC___________G___AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	266 -- 272	13 -- 19	-11.4583 kcal/mol	2.34189 kcal/mol	1.23906 kcal/mol	264 279@LB@ \| \|@LB@5'-CAA...ACUUA C AAAAU...UGC-3'@LB@ GUAACAAA UG GCG@LB@ :\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UAUUGUUU AC CGC@LB@3'-UUU...ACUAC G AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -11.4583 kcal/mol@LB@Unfolding Energy - mRNA 2.34189 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 265 -- 278@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 13 -- 19@LB@
97	0.009805	0.3104	b1306	pspC	-10.74	0.090670	128 -- 139	7 -- 18	psp operon transcription co-activator		_____________127__________140\n_____________\|____________\|\n5'-CCG...AGCAA____________AACGU...CGG-3'\n______________AACGGAUGCGCG\n______________\|\|\|::\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	133 -- 139	7 -- 13	-18.5075 kcal/mol	6.55818 kcal/mol	1.20891 kcal/mol	127 140@LB@ \| \|@LB@5'-CCG...AGCAA AACGU...CGG-3'@LB@ AACGGAUGCGCG@LB@ \|\|\|::\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.5075 kcal/mol@LB@Unfolding Energy - mRNA 6.55818 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@LB@
105	0.01074	0.3104	b3791	wecE	-13.91	0.024834	1 -- 12	7 -- 18	TDP-4-oxo-6-deoxy-D-glucose transaminase		______________1___________13\n______________\|___________\|\n___________5'-____________AAUUG...CCC-3'\n______________GACAGAUGCGCG\n______________:\|\|\|:\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	6 -- 12	7 -- 13	-19.4696 kcal/mol	4.34626 kcal/mol	1.20891 kcal/mol	1 13@LB@ \| \|@LB@ 5'- AAUUG...CCC-3'@LB@ GACAGAUGCGCG@LB@ :\|\|\|:\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -19.4696 kcal/mol@LB@Unfolding Energy - mRNA 4.34626 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 7 -- 13@LB@
107	0.01107	0.3104	b0723	sdhA	-7.08	0.348281	169 -- 200	7 -- 42	succinate dehydrogenase flavoprotein subunit		_____________168__________________________________201\n_____________\|____________________________________\|\n5'-GGU...ACGUG____A________UU_______UG____________AUGAA...GUG-3'\n______________AUUU_UGGAUUCG___GUGGUG_____GGGUGUGUG\n______________\|\|:\|_\|\|:\|\|\|\|:___:\|\|:\|\|_____:::\|\|:\|:\|\n______________UAGA_ACUUAAGU___UACUAC_____UUUACGCGC\n3'-UUU...UAAAG____G________CCC______UAUUG_________AGAAAG-5'\n_____________\|____________________________________\|\n_____________43___________________________________6\n	194 -- 200	7 -- 13	-22.2639 kcal/mol	5.75915 kcal/mol	9.42962 kcal/mol	168 201@LB@ \| \|@LB@5'-GGU...ACGUG A UU UG AUGAA...GUG-3'@LB@ AUUU UGGAUUCG GUGGUG GGGUGUGUG@LB@ \|\|:\| \|\|:\|\|\|\|: :\|\|:\|\| :::\|\|:\|:\|@LB@ UAGA ACUUAAGU UACUAC UUUACGCGC@LB@3'-UUU...UAAAG G CCC UAUUG AGAAAG-5'@LB@ \| \|@LB@ 43 6@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -22.2639 kcal/mol@LB@Unfolding Energy - mRNA 5.75915 kcal/mol@LB@Unfolding Energy - sRNA 9.42962 kcal/mol@LB@@LB@Position - mRNA 169 -- 200@LB@Position - sRNA 7 -- 42@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 7 -- 13@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation		_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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